Yes I understand your confusion with the diagram, but in fact that's not an antiquark there... it's a squark [scalar]. The thing above is not a bar [indicating anti- ] but a tilde [indicating super-]. You can zoom in and see it by yourself, at some point it becomes pretty obvious :)
The coupling is then with quark-quark-squark.
If you allowed a vertex with quark-quark-antiquark then your Lagrangian would need to have a term with fields containing those 3 particles- to make it simple let's say it has the fields \mathcal{L}= q_1 q_2 \bar{q}_3 so that's a 3 \otimes 3 \otimes \bar{3} term which violates the SU[3] symmetry. SU[3] permits only 3 \otimes \bar{3} (eg in a mass term) or 3 \otimes 3 \otimes 3 and of course \bar{3} \otimes \bar{3} \otimes \bar{3} , or in general words: configurations which have the singlet representation as a result , so they can be SU[3] invariant. That's how you build the MSSM: send your SM fields to chiral superfields existing in the same representations as in SM, take SU(3)xSU(2)xU(1) and start building up your model's lagrangian which has those invariant terms.
The RPV terms then naturally appear in the model (so they are singlets) as well as the rest MSSM interaction terms...
For SU(2):
It is a singlet, since U,U and D are singlets. So you have 1 \otimes 1 \otimes 1...
In case you have the one singlet and put a doublet like for example the Q, you also need to put a 2nd doublet (like L) to keep SU(2) invariance- in fact the one is bared but it doesn't make a big difference for SU(2) since the fundamental and antifundamental reprs are the same- : 2 \otimes 2 \otimes 1 = ( 3 \oplus 1 ) \otimes 1 = 3 \oplus 1 which can be SU(2) invariant.
(Sad personal fact:
:( this way of configurations of representations costed me a whole question to my SUSY exams and lost a very good grade, where I had to find those RPV terms and explain the need for R-parity afterwards with diagrams, and I messed up the fields resulting in non-SU(3) x SU(2) x U(1) invariant quantities... when I asked for some compassion especially because I couldn't see why 3x3x3 is a singlet, I was told "you shouldn't have tried SUSY if you don't know this trivial stuff" - of course I did know, but during the exam I had forgotten. Also during the exam they also tried to help us saying "thing of protons and pions" but it was more confusing than helpful during the exam time. Well although the mark was "bad" for me, I learned out of it.
)